Nanotechnology is a promising new field which has brought new frontiers in many fields of research and technology. Nanoencapsulation is one of such modern techniques based on enclosing a bioactive compound in a matrix of inert material. Natural products that are both primary and secondary metabolites are of immense use; nanoencapsulation of these would make them more efficacious. By using this technique, natural product can be entrapped and preserved. This technique also enhances their property, improves regulation and release in physiologically active sites, and imparts improved bioavailability. Nanoencapsulation is used in designing effective drug delivery systems. The nanoencapsulated natural product is used in food production, packaging, storing, processing, industry, drug delivery systems, and clinical trials more effectively. Though many studies have been done on nanoencapsulation but it still needs to be popularized. This chapter depicts different nanoencapsulation methods, their examples, and synthesis of nanomaterial. Classification of the nanoencapsulation systems, benefits and trending new approaches of nanoencapsulation of natural products, nanocapsules bioavailability, safety and regulatory issues of nanoencapsulated products, and challenges and future perspectives are also discussed.